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URL: https://einarolafsson.github.io/spacr/
Proper Citation: spaCR (RRID:SCR_029041)
Description: Software Python framework that links pooled CRISPR-Cas9 perturbations to single-cell spatial phenotypes. It segments cells, nuclei, pathogens and organelles in high-content microscopy images with Cellpose, measures morphology, intensity, texture, spatial and colocalization features into a single SQLite project, supports keyboard-driven annotation and active learning, trains image and measurement-based classifiers with held-out performance recorded per checkpoint, maps sequencing reads to wells and gRNA barcodes, and estimates per-guide and per-gene effects by multiple linear regression to produce a ranked hit list. It runs as a Qt desktop application or headlessly on a workstation, server or cluster, on Linux, macOS and Windows, with CUDA, ROCm, Metal and Intel XPU acceleration.
Abbreviations: spaCR
Synonyms: , spacr; spaCR: spatial phenotype analysis of CRISPR screens
Resource Type: 1d time-series analysis software, data analysis software, data processing software, software application, software resource, time-series analysis software
Defining Citation: PMID:42465465
Keywords: CRISPR screen; pooled screen; image-based screening; high-content screening; spatial phenotype; single-cell; cell segmentation; Cellpose; deep learning; image classification; barcode mapping; regression; host-pathogen; Toxoplasma gondii; microscopy; Python; SQLite
Funding: NIAID AI007413; NIAID AI180278; NIGMS GM151129; NIH Office of the Director OD034245; Swedish Research Council 2021-06749
Availability: Free, Available for download, Freely available
Resource Name: spaCR
Resource ID: SCR_029041
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Source: SciCrunch Registry (RRID:SCR_005400)
Description: Interactive portal for finding and submitting biomedical resources. Resources within SciCrunch have assigned RRIDs which are used to cite resources in scientific manuscripts. SciCrunch Registry, formerly NIF Registry, provides resources catalog. Allows to add new resources. Allows edit existing resources after registration. Curators are tasked with identifying and registering resources, examining data, writing configuration files to index and display data and keeping contents current.
URL: https://rrid.site/rin/sources/SCR_005400
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